|
| Status |
Public on Jun 04, 2020 |
| Title |
gelatin_std_2 |
| Sample type |
SRA |
| |
|
| Source name |
C57BL6/J WT mESC
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL6/J
cell type: Embryonic stem cell
culture condition: gelatin coated dish under Std medium
|
| Growth protocol |
WT mESCs derived from inbred mouse (Bruce 4 C57BL/6J, male, EMD Millipore, Billerica, MA) were cultured on either LN511 or gelatin coated dish under either Std or 2i medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
C57BL/6J WT mESCs were conditioned on either gelatin or LN511 coated dish in either Std or 2i medium for 2 weeks.
Then, RNA was recovered from 1x106 cells using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
gelatin_std_2_GGCTAC_L001
|
| Data processing |
All reads are mapped to mm10 using TopHat (version 2.1.1)
FPKM are quantified using Cufflinks (version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: genes.fpkm.csv and isoforms.fpkm.csv files include RPKM values at gene- and transcript-level, respectively
|
| |
|
| Submission date |
Jun 12, 2019 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Itoshi NIKAIDO |
| E-mail(s) |
itoshi.nikaido@riken.jp
|
| Organization name |
RIKEN
|
| Department |
Center for Biosystems Dynamics Research
|
| Lab |
Laboratory for Bioinformatics Research
|
| Street address |
2-1 Hirosawa
|
| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE132591 |
RNA-seq analysis of mESCs cultured on either Laminin-511 or gelatin coated dishes in either Std or 2i medium |
| GSE132593 |
Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells |
|
| Relations |
| BioSample |
SAMN12037552 |
| SRA |
SRX6047931 |
